I'm using iOS 9.2 and I once accidentally tapped “don't allow” or something similar when WhatsApp was opening a link for Citymapper. It used to launch the Citymapper app, but now it goes to the less useful web interface.
I've looked through all the settings but I can't find any record of this preference to reset the permission.
Metadata on page:
<meta property="al:ios:url" content="citymapper://directions?endcoord=51.56819%2C-0.086512®ion_id=uk-london" />
<meta property="al:ios:app_store_id" content="469463298" />
<meta property="al:ios:app_name" content="Citymapper" />
<meta property="al:android:package" content="com.citymapper.app.release" />
<meta property="al:android:app_name" content="Citymapper" />
<meta property="al:android:url" content="citymapper://directions?endcoord=51.56819%2C-0.086512®ion_id=uk-london" />
Best Answer
If I'm reading the documentation correctly, when the web interface pops up in Safari, there should be a banner across the top of the page that essentially says, "Hey, you could view this info in the app instead!" If you tap OPEN on that banner, it's supposed to re-establish the universal linking to the app instead of the website. Here it is in Apple's words:
Source: Universal Links in Apple's App Search Programming Guide